PsychENCODE’s marker gene selection might be imperfect since some “marker” genes are shared by different cell types. However, it has enough discriminatory power. Using this initial dictionary of marker genes, we can start analyzing 10x data, which consist of these three files:
## %%MatrixMarket matrix coordinate integer general
## 17926 70634 119696200
## 56 1 1
## 139 1 1
## 270 1 1
## 324 1 1
## 375 1 1
## 389 1 1
## 420 1 1
## 557 1 1
## AAACGGGAGATCCCGC.1
## AAATGCCTCCAATGGT.1
## AACCATGTCAGTGCAT.1
## AACCATGTCTGTACGA.1
## AACCGCGTCCGCATAA.1
## AACGTTGGTTCAGGCC.1
## AACTGGTGTACCGGCT.1
## AAGACCTAGTTAACGA.1
## AAGGAGCAGCAATCTC.1
## AAGGAGCTCTGCTGCT.1
## FO538757.2
## SAMD11
## NOC2L
## KLHL17
## PLEKHN1
## PERM1
## HES4
## ISG15
## AGRN
## RNF223
## Joining, by = "ct"
377 genes (2.72%) consist of 123 found in Ex, 36 found in In, 86 found in Oligo, 58 found in OPC, 24 found in Microglia, 57 found in Astro
28 genes (0.2%) consist of 5 found in Ex, 4 found in In, 6 found in Oligo, 6 found in OPC, 2 found in Microglia, 5 found in Astro
13848 genes in total.
## quartz_off_screen
## 2
## Warning: Removed 4702 rows containing non-finite values (stat_smooth).
## Warning: Removed 4702 rows containing non-finite values (stat_cor).
## Warning: Removed 4702 rows containing missing values (geom_point).
## Warning: ggrepel: 8 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
## Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
## Warning: ggrepel: 6 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
## Warning: ggrepel: 6 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
## Warning: ggrepel: 6 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
## Warning: ggrepel: 1 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps